EHV-1 Genes’ transcript ratios
Balázs Kakuk
## Error in read.table(file = file, header = header, sep = sep, quote = quote, :
## object 'config' not foundProject info
Samples: dcDNA Seq
pychopper: no
mapping version: v6
LoRTIA: yes (stranded only)
Filtering samples: C6_2h_3 & PC-12_8h_3
Only those reads were counted, where LoRTIA found both 5- and 3-prime adapters!
Correct some genes in the annotation
DO NOT Filter second copies of genes, as in some cases there are transcripts from only one of the copies
Counts based on iterative GFF-compare results
This was done as follows:
The reference transcripts were compared individually/iteratively to the reads.
The distances between the reads and each reference transcript hit were calculated.
For each read, the most similar reference transcript was assigned (lowest distance).
Additionally, these distances must had fulfill the following rules: max prime5 distance <= 10
max prime3 distance <= 10
exon/intron junction difference <= 2Thus based on these, the read counts for each reference transcript were assessed.
The transcripts were then assigned to their parent genes (by Torma G) and their ratio (isoform ratio) was calculated as follows:
isoform ratio = transcript isoform count / total gene countThose reads that could not be assigned to the reference transcripts were assigned to their parent genes, based on their 5-prime ends and independently to their parent gene cluster, based on their 3-prime ends.
So the reads are either:
- assigned to a reference transcript
- could not not be assigned to a ref TR, in which case they were:
- assigned to their parent gene based on their 5-prime end
overlapping with the gene’s TSS
- assigned to their parent gene-cluster based on their
3-prime end overlapping with the cluster’s TES
- assigned to both
- assigned to their parent gene based on their 5-prime end
overlapping with the gene’s TSS
1. Kinetics of Reference Transcript Isoforms, according to their host gene
The reads were assigned to their parent gene based on their
5-prime end overlapping with the gene’s TSS
(but not necessarily with the gene cluster’s TES)
## NULLMerge annotation with RefClass
Exclude those ref transcripts that were not observed (or observed under the threshold) from the annotation as well
Evaluate CAGE against dcDNA read counts
## Key: <transcript_id>
## Empty data.table (0 rows and 36 cols): transcript_id,CAGE_ID,score,support,CAGE_significance,seqnames...
## gene N
## <char> <int>
## 1: CTO 7799
## 2: NOIR 10766
## 3: ORF1 3004
## 4: ORF10 2242
## 5: ORF11 13394
## 6: ORF12 7041
## 7: ORF13 1437
## 8: ORF14 17457
## 9: ORF19 9218
## 10: ORF23 6801
## 11: ORF24 8431
## 12: ORF28 479
## 13: ORF27 1650
## 14: ORF29 3365
## 15: ORF3 3585
## 16: ORF31 3707
## 17: ORF32 7141
## 18: ORF33 3100
## 19: ORF34 13265
## 20: ORF38 8266
## 21: ORF39 6484
## 22: ORF8 5526
## 23: ORF40 5624
## 24: ORF41 550
## 25: ORF42 13205
## 26: ORF43 30295
## 27: ORF45 551
## 28: ORF46 7027
## 29: ORF48 560
## 30: ORF49 1797
## 31: ORF50 2420
## 32: ORF51 5714
## 33: ORF53 7564
## 34: <NA> 21256
## 35: ORF54 10621
## 36: ORF57 8358
## 37: ORF58 31916
## 38: ORF64 11121
## 39: ORF65 18521
## 40: ORF66 3046
## 41: ORF67 19946
## 42: ORF69 844
## 43: ORF70 4555
## 44: ORF71 11767
## 45: ORF72 2719
## 46: ORF73 6459
## 47: ORF74 1269
## 48: ORF75 3872
## 49: ORF76 769
## 50: ORF17 4701
## 51: ORF35 3083
## 52: ORF15 9679
## 53: ORF9 11057
## 54: ORF16 3220
## 55: ORF18 12641
## 56: ORF2 4130
## 57: ORF20 8207
## 58: ORF21 1072
## 59: ORF22 11355
## 60: ORF25 6854
## 61: ORF26 1861
## 62: ORF30 5787
## 63: ORF35.5 5778
## 64: ORF36 4161
## 65: ORF37 2706
## 66: ORF4 1933
## 67: ORF44 8836
## 68: ORF5 6844
## 69: ORF52 12355
## 70: ORF55 3656
## 71: ORF56 853
## 72: ORF59 10235
## 73: ORF6 1713
## 74: ORF60 3352
## 75: ORF61 947
## 76: ORF62 2723
## 77: ORF63 9807
## 78: ORF68 1737
## 79: ORF7 239
## gene N## gene class_code N
## <char> <char> <int>
## 1: <NA> = 58## Key: <gene>
## gene 3`-long 3`-short 5`-long 5`-short = Splice-variant c e
## <char> <int> <int> <int> <int> <int> <int> <int> <int>
## 1: <NA> 207 256 59 309 58 14 388 2
## 2: CTO 93 61 1790 2085 424 681 85 NA
## 3: NOIR 166 62 1522 784 531 123 388 1645
## 4: ORF1 12 97 534 1237 159 79 79 NA
## 5: ORF10 32 228 145 755 221 81 130 NA
## 6: ORF11 115 450 1883 6530 660 207 957 NA
## 7: ORF12 59 451 382 3904 238 140 619 NA
## 8: ORF13 2 448 48 148 122 402 17 NA
## 9: ORF14 5 907 2739 4325 412 281 2780 NA
## 10: ORF15 20 970 3282 3008 355 255 327 NA
## 11: ORF16 11 983 182 773 419 356 79 NA
## 12: ORF17 90 133 154 2397 145 7 293 NA
## 13: ORF18 45 428 3288 3110 419 491 296 NA
## 14: ORF19 3 154 1015 6090 350 131 518 NA
## 15: ORF2 8 140 350 2617 206 23 400 NA
## 16: ORF20 3 257 1374 4928 195 76 540 NA
## 17: ORF21 3 148 64 357 121 70 60 NA
## 18: ORF22 19 423 587 7926 325 210 429 NA
## 19: ORF23 15 189 1888 2630 209 48 287 NA
## 20: ORF24 21 107 1586 3128 246 44 852 NA
## 21: ORF25 94 921 1121 2703 287 501 260 NA
## 22: ORF26 2 84 307 870 131 23 94 NA
## 23: ORF27 5 23 175 270 58 11 100 NA
## 24: ORF28 NA 28 34 168 45 13 40 NA
## 25: ORF29 37 513 529 1399 190 119 135 NA
## 26: ORF3 5 88 390 2552 133 29 147 NA
## 27: ORF30 2 55 1766 1652 184 47 74 NA
## 28: ORF31 4 872 216 1273 178 276 331 NA
## 29: ORF32 13 89 119 965 101 11 197 NA
## 30: ORF33 31 296 111 1166 259 194 622 NA
## 31: ORF34 24 464 486 4611 292 199 574 NA
## 32: ORF35 4 9 333 673 34 9 40 NA
## 33: ORF35.5 33 805 510 2464 237 241 517 NA
## 34: ORF36 32 263 259 2265 188 73 394 NA
## 35: ORF37 17 65 420 1128 157 40 108 NA
## 36: ORF38 2 129 905 5330 463 97 440 NA
## 37: ORF39 32 77 2500 1878 201 61 334 NA
## 38: ORF4 4 70 371 1088 142 8 57 NA
## 39: ORF40 28 545 359 2279 334 307 452 NA
## 40: ORF41 2 149 59 35 103 40 20 NA
## 41: ORF42 67 3804 182 1625 383 1650 1878 NA
## 42: ORF43 73 1577 2266 6919 466 235 9213 NA
## 43: ORF44 3 115 2157 2746 476 54 117 45
## 44: ORF45 NA 75 93 81 110 72 11 NA
## 45: ORF46 8 199 596 4510 156 45 414 NA
## 46: ORF48 2 68 52 162 151 45 7 NA
## 47: ORF49 2 24 165 373 77 15 114 NA
## 48: ORF5 4 201 705 4755 197 67 358 NA
## 49: ORF50 1 168 289 1195 179 33 227 NA
## 50: ORF51 12 142 3321 827 206 14 45 NA
## 51: ORF52 5 550 478 7450 263 431 1147 NA
## 52: ORF53 37 123 115 196 138 27 1921 1265
## 53: ORF54 576 1152 637 4288 483 496 1526 NA
## 54: ORF55 14 35 1046 723 92 7 154 NA
## 55: ORF56 2 27 29 80 54 19 52 NA
## 56: ORF57 39 260 1840 2039 547 24 1069 NA
## 57: ORF58 12 1415 7693 11551 1099 796 1126 NA
## 58: ORF59 47 788 1071 5297 459 338 910 NA
## 59: ORF6 6 547 231 252 202 158 53 NA
## 60: ORF60 10 578 700 785 375 396 105 NA
## 61: ORF61 2 199 183 172 96 59 54 NA
## 62: ORF62 3 877 94 325 180 327 103 NA
## 63: ORF63 1 384 501 4870 133 293 1425 NA
## 64: ORF64 NA 144 30 6617 46 64 1278 NA
## 65: ORF65 46 2643 3775 4989 1460 2003 392 9
## 66: ORF66 6 130 452 1640 184 24 74 NA
## 67: ORF67 14 1268 1196 10435 384 533 3374 NA
## 68: ORF68 NA 193 212 419 111 119 182 NA
## 69: ORF69 28 126 92 55 67 72 63 NA
## 70: ORF7 NA 1 35 107 20 5 6 NA
## 71: ORF70 51 111 418 2472 188 52 248 NA
## 72: ORF71 29 745 2299 3021 287 104 821 NA
## 73: ORF72 16 124 455 684 209 113 38 NA
## 74: ORF73 2 113 767 3700 111 26 664 NA
## 75: ORF74 27 33 37 600 95 30 123 NA
## 76: ORF75 30 211 473 2403 189 91 92 NA
## 77: ORF76 NA 140 45 191 97 86 66 NA
## 78: ORF8 10 218 1153 2770 296 62 216 NA
## 79: ORF9 17 185 682 2008 272 73 359 NA
## gene 3`-long 3`-short 5`-long 5`-short = Splice-variant c e
## i j k m n o p x y ~
## <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
## 1: NA 18 69 12 NA 1007 281 18475 13 88
## 2: NA NA 167 NA NA 479 22 1855 NA 57
## 3: NA 155 154 1276 254 2043 35 522 618 488
## 4: NA NA 294 NA NA 353 NA 93 2 65
## 5: NA NA 2 NA NA 205 NA 244 NA 199
## 6: NA NA 34 NA NA 742 87 828 NA 901
## 7: NA NA 9 NA NA 507 9 518 NA 205
## 8: NA NA NA NA NA 170 NA 67 NA 13
## 9: NA NA 233 NA NA 2655 NA 2682 NA 438
## 10: NA NA 141 NA NA 662 NA 242 NA 417
## 11: NA NA 2 NA NA 208 NA 143 NA 64
## 12: NA NA 59 NA NA 171 302 679 1 270
## 13: NA NA 350 NA NA 2311 36 1620 NA 247
## 14: NA NA 3 NA NA 559 NA 258 NA 137
## 15: NA NA 5 NA NA 87 46 138 NA 110
## 16: NA NA 12 NA NA 435 13 226 NA 148
## 17: NA NA 2 NA NA 65 NA 166 NA 16
## 18: NA NA 11 NA NA 840 37 461 1 86
## 19: NA NA 135 NA NA 411 237 574 NA 178
## 20: NA NA 284 NA NA 535 147 1313 2 166
## 21: NA NA 66 NA NA 320 32 406 NA 143
## 22: NA NA 2 NA NA 132 NA 165 NA 51
## 23: NA NA 36 NA NA 144 31 777 1 19
## 24: NA NA 2 NA NA 30 NA 113 NA 6
## 25: NA NA 39 NA NA 251 NA 83 NA 70
## 26: NA NA 12 NA NA 81 NA 58 NA 90
## 27: NA NA 59 NA NA 381 NA 1466 NA 101
## 28: NA NA 5 NA NA 211 NA 323 NA 18
## 29: NA NA 9 NA NA 112 15 5467 NA 43
## 30: NA NA NA NA NA 187 NA 180 NA 54
## 31: NA NA 15 NA NA 426 96 5933 1 144
## 32: NA NA 12 NA NA 300 8 1605 NA 56
## 33: NA NA 4 NA NA 633 NA 208 NA 126
## 34: NA NA 3 NA NA 150 NA 454 NA 80
## 35: NA NA 11 NA NA 305 54 306 NA 95
## 36: NA 31 3 15 1 150 42 472 27 159
## 37: NA NA 351 NA NA 185 NA 609 NA 256
## 38: NA NA 12 NA NA 34 NA 84 1 62
## 39: NA NA 6 NA NA 589 1 564 22 138
## 40: NA NA NA NA NA 76 NA 60 NA 6
## 41: NA NA 1 NA NA 1323 NA 2196 NA 96
## 42: NA NA 35 NA NA 2798 133 6077 2 501
## 43: 8 143 50 696 12 70 22 1895 13 214
## 44: NA NA NA NA NA 75 NA 27 NA 7
## 45: NA NA 17 NA NA 383 129 499 NA 71
## 46: NA NA NA NA NA 29 NA 29 NA 15
## 47: NA NA 26 NA NA 203 181 595 NA 22
## 48: NA NA NA NA NA 317 NA 158 NA 82
## 49: NA NA 3 NA NA 142 NA 136 NA 47
## 50: NA NA 407 NA NA 296 33 343 NA 68
## 51: NA NA 1 NA NA 1027 NA 714 NA 289
## 52: 20 9 4 2644 1 515 37 475 NA 37
## 53: NA 216 63 NA 14 350 NA 334 NA 486
## 54: NA NA 80 NA NA 90 NA 1369 NA 46
## 55: NA NA 3 NA NA 17 NA 559 NA 11
## 56: NA NA 137 NA NA 716 3 1204 NA 480
## 57: 134 571 436 86 141 3460 4 1133 70 2189
## 58: NA NA 2 NA NA 623 NA 265 NA 435
## 59: NA NA 1 NA NA 96 NA 139 NA 28
## 60: NA NA 2 NA NA 232 NA 88 NA 81
## 61: NA NA NA NA NA 86 NA 73 NA 23
## 62: NA NA 33 NA NA 548 NA 210 1 22
## 63: NA NA 8 NA NA 1622 90 418 1 61
## 64: NA NA NA NA NA 960 189 1779 NA 14
## 65: NA 205 26 133 5 809 8 1162 4 852
## 66: NA NA 8 NA NA 102 6 368 NA 52
## 67: NA NA 99 NA NA 1516 NA 259 2 866
## 68: NA NA 2 NA NA 400 NA 62 1 36
## 69: NA NA 4 NA NA 66 NA 250 NA 21
## 70: NA NA NA NA NA 51 NA 2 NA 12
## 71: NA NA 35 NA NA 312 273 322 NA 73
## 72: NA NA 265 NA NA 523 NA 3482 NA 191
## 73: NA NA 193 NA NA 357 1 438 6 85
## 74: NA NA 9 NA NA 665 NA 227 NA 175
## 75: NA NA 7 NA NA 85 NA 178 1 53
## 76: NA NA 14 NA NA 163 45 128 NA 33
## 77: NA NA NA NA NA 66 NA 69 1 8
## 78: NA 29 36 NA NA 182 NA 448 47 59
## 79: 2 119 46 20 5 731 9 6398 45 86
## i j k m n o p x y ~
There are many transcripts that were identifed with CAGE, and have a high read count in the dcDNA but are novel (not in the reference). They are not the product of false 5-prime sites as they have correct TSS adapaters. Most of these are antisense or 5-prime short but there are 5-prime longs (both shere the 4-primes with ref transcripts) and ‘c’ as well (which have different 3-primes)
Lets check them gene-wise The 5-prime long and short variants.
It seems that ORF51 particularly has a lot of these Check the novel long
isoforms for this gene first
Select TSS clusters that are significant (non-NA) in the CAGE results AND have sufficient read counts in the dcDNA reads as well, from where their 5-prime ends were correct and their class-code based on gff-compare was either 5-prime short or long.
Exclude those transfrags that have more than one exon, for now.
## [1] 10837## [1] 252## [1] 954 1224 2246 2261 3011 3014 3327 4014 3344 3394 3458 2228 3385 96 132
## [16] 134 166 193 413 415 657 687 704 725 805 1105 1354 1477 1496 1715
## [31] 1733 2337 3343 1004 2714 275 313 400 500 644 771 878 1027 1542 1894
## [46] 2185 2308## [1] FALSE## [1] TRUE## CAGE_cluster_width N
## <num> <int>
## 1: 1 4564
## 2: 2 654
## 3: 3 1624
## 4: 4 1983
## 5: 5 1117
## 6: 6 7498
## 7: 7 3975
## 8: 8 1624
## 9: 9 3108
## 10: 10 1983
## 11: 11 1174
## 12: 12 1129
## 13: 13 2358
## 14: 14 1176
## 15: 15 1114
## 16: 16 1473
## 17: 17 1533
## 18: 18 1059
## 19: 19 1010
## 20: 20 983
## 21: 21 714
## 22: 22 412
## 23: 23 551
## 24: 24 453
## 25: 25 1416
## 26: 26 1443
## 27: 27 1072
## 28: 28 202
## 29: 29 1017
## 30: 30 229
## 31: 31 1437
## 32: 32 1539
## 33: 33 1385
## 34: 34 3477
## 35: 35 1048
## 36: 36 984
## 37: 37 2146
## 38: 38 3796
## 39: 39 3981
## 40: 40 232
## 41: 41 236
## 42: 42 1638
## 43: 43 1602
## 44: 44 635
## 45: 45 727
## 46: 46 21
## 47: 48 603
## 48: 51 1433
## 49: 52 202
## 50: 53 646
## 51: 54 1040
## 52: 55 1943
## 53: 57 2361
## 54: 59 607
## 55: 60 385
## 56: 65 902
## 57: 67 573
## 58: 70 1444
## 59: 72 1102
## 60: 74 260
## 61: 77 3796
## 62: 78 6256
## 63: 82 1795
## 64: 86 932
## 65: 90 874
## 66: 128 496
## 67: 170 5018
## 68: 222 2305
## 69: 231 4432
## 70: NA 425089
## CAGE_cluster_width N
## [1] 576## seqnames strand TX_nov_ID sum_count
## <char> <char> <char> <int>
## 1: NC_001491.2 + TX_nov_ID_103 315
## 2: NC_001491.2 + TX_nov_ID_715 644
## 3: NC_001491.2 + TX_nov_ID_720 541
## 4: NC_001491.2 + TX_nov_ID_721 437
## 5: NC_001491.2 + TX_nov_ID_614 92
## ---
## 1250: NC_001491.2 - TX_nov_ID_1026 1
## 1251: NC_001491.2 - TX_nov_ID_857 1
## 1252: NC_001491.2 - TX_nov_ID_926 1
## 1253: NC_001491.2 - TX_nov_ID_1222 1
## 1254: NC_001491.2 - TX_nov_ID_982 1## transcript_id Ref_Class gene gene_cluster gene_region
## <char> <char> <char> <char> <char>
## 1: CTO-L CTO-L CTO CTO CTO
## 2: CTO-S CTO-S CTO CTO CTO
## 3: CTO-S-AS CTO-S-AS CTO <NA> CTO
## 4: NOIR-2-canonic NOIR-2-canonic NOIR NOIR NOIR
## 5: NOIR-Canonic NOIR-Canonic NOIR NOIR_1 NOIR_1
## ---
## 580: nct65-Canonic nct65-Canonic ORF65 ORF65_1 ORF65_1
## 581: nct65-Long nct65-Long ORF65 ORF65_1 ORF65_1
## 582: nct65-Short nct65-Short ORF65 ORF65_1 ORF65_1
## 583: nct65.1-Canonic nct65.1-Canonic ORF65 ORF65 ORF65
## 584: nct65.1-Long nct65.1-Long ORF65 ORF65 ORF65
## seqnames strand exon_number start.TR end.TR start.exon end.exon start
## <char> <char> <int> <int> <int> <int> <int> <int>
## 1: NC_001491.2 - 1 73834 74257 73834 74257 73834
## 2: NC_001491.2 - 1 73834 74183 73834 74183 73834
## 3: NC_001491.2 + 1 73856 74182 73856 74182 73856
## 4: NC_001491.2 - 1 143303 144282 143303 144282 143303
## 5: NC_001491.2 + 1 118878 119857 118878 119857 118878
## ---
## 580: NC_001491.2 + 1 122066 122451 122066 122451 122066
## 581: NC_001491.2 + 1 121788 122451 121788 122451 121788
## 582: NC_001491.2 + 1 122258 122451 122258 122451 122258
## 583: NC_001491.2 - 1 140709 141094 140709 141094 140709
## 584: NC_001491.2 - 1 140709 141372 140709 141372 140709
## end prime5.TR prime5.ex prime3.TR prime3.ex last_exon source
## <int> <int> <int> <int> <int> <lgcl> <char>
## 1: 74257 74257 74257 73834 73834 TRUE Torma_et_al
## 2: 74183 74183 74183 73834 73834 TRUE Torma_et_al
## 3: 74182 73856 73856 74182 74182 TRUE Torma_et_al
## 4: 144282 144282 144282 143303 143303 TRUE Torma_et_al
## 5: 119857 118878 118878 119857 119857 TRUE Torma_et_al
## ---
## 580: 122451 122066 122066 122451 122451 TRUE Torma_et_al
## 581: 122451 121788 121788 122451 122451 TRUE Torma_et_al
## 582: 122451 122258 122258 122451 122451 TRUE Torma_et_al
## 583: 141094 141094 141094 140709 140709 TRUE Torma_et_al
## 584: 141372 141372 141372 140709 140709 TRUE Torma_et_al
## CAGE.cluster.start CAGE.cluster.end CAGE_ID support score
## <int> <int> <char> <int> <num>
## 1: 74257 74257 CAGE_cluster_1531 3 414.7285
## 2: 73985 74215 CAGE_cluster_1530 9 196155.6857
## 3: NA NA NA NA
## 4: 144255 144308 CAGE_cluster_1896 9 24468.6633
## 5: 118852 118905 CAGE_cluster_835 9 24468.6633
## ---
## 580: 121909 122130 CAGE_cluster_860 8 12115.5339
## 581: 121767 121848 CAGE_cluster_858 8 6916.8878
## 582: 122244 122310 CAGE_cluster_862 9 12391.8990
## 583: 141030 141251 CAGE_cluster_1871 8 12115.5339
## 584: 141312 141393 CAGE_cluster_1873 8 6916.8878
## CAGE_significance thick.start thick.end
## <char> <int> <int>
## 1: ** 74257 74257
## 2: *** 74183 74183
## 3: NA NA
## 4: *** 144282 144282
## 5: *** 118878 118878
## ---
## 580: *** 121935 121935
## 581: *** 121783 121783
## 582: *** 122259 122259
## 583: *** 141225 141225
## 584: *** 141377 141377## cmp_ref seqnames strand gene sample gene_region
## <char> <char> <char> <char> <char> <char>
## 1: NOIR-Canonic NC_001491.2 + NOIR EHV-1_12h_1 NOIR_1
## 2: NOIR-Canonic NC_001491.2 + NOIR EHV-1_12h_2 NOIR_1
## 3: NOIR-Canonic NC_001491.2 + NOIR EHV-1_12h_3 NOIR_1
## 4: NOIR-Canonic NC_001491.2 + NOIR EHV-1_18h_1 NOIR_1
## 5: NOIR-Canonic NC_001491.2 + NOIR EHV-1_18h_2 NOIR_1
## ---
## 12848: as9 NC_001491.2 - ORF9 EHV-1_6h_2 ORF9
## 12849: as9 NC_001491.2 - ORF9 EHV-1_6h_3 ORF9
## 12850: as9 NC_001491.2 - ORF9 EHV-1_8h_1 ORF9
## 12851: as9 NC_001491.2 - ORF9 EHV-1_8h_2 ORF9
## 12852: as9 NC_001491.2 - ORF9 EHV-1_8h_3 ORF9
## Kinetic_class Ref_Class class_code read_count hpi Time cell_line
## <fctr> <char> <char> <int> <fctr> <int> <fctr>
## 1: unknown NOIR-Canonic = 82 12h 12 RK-13
## 2: unknown NOIR-Canonic = 55 12h 12 RK-13
## 3: unknown NOIR-Canonic = 61 12h 12 RK-13
## 4: unknown NOIR-Canonic = 26 18h 18 RK-13
## 5: unknown NOIR-Canonic = 20 18h 18 RK-13
## ---
## 12848: L as9 = 0 6h 6 RK-13
## 12849: L as9 = 0 6h 6 RK-13
## 12850: L as9 = 0 8h 8 RK-13
## 12851: L as9 = 0 8h 8 RK-13
## 12852: L as9 = 0 8h 8 RK-13
## group gene_cluster parent norm_base
## <char> <char> <char> <num>
## 1: RK-13_12h NOIR_1 <NA> 1
## 2: RK-13_12h NOIR_1 <NA> 1
## 3: RK-13_12h NOIR_1 <NA> 1
## 4: RK-13_18h NOIR_1 <NA> 1
## 5: RK-13_18h NOIR_1 <NA> 1
## ---
## 12848: RK-13_6h ORF9 <NA> 1
## 12849: RK-13_6h ORF9 <NA> 1
## 12850: RK-13_8h ORF9 <NA> 1
## 12851: RK-13_8h ORF9 <NA> 1
## 12852: RK-13_8h ORF9 <NA> 1## Key: <sample>
## Index: <transcript_id>
## sample transcript_id cmp_ref class_code gene CAGE_ID
## <char> <int> <char> <char> <char> <char>
## 1: EHV-1_12h_1 2 ORF75 5`-short ORF75 CAGE_cluster_987
## 2: EHV-1_12h_1 3 ORF15 = ORF15 CAGE_cluster_1205
## 3: EHV-1_12h_1 3 ORF15 = ORF15 CAGE_cluster_1205
## 4: EHV-1_12h_1 4 ORF67.1 5`-short ORF67 <NA>
## 5: EHV-1_12h_1 4 ORF67.1 5`-short ORF67 <NA>
## ---
## 1291331: EHV-1_8h_3 538397 ORF14-L4 x ORF14 <NA>
## 1291332: EHV-1_8h_3 538401 ORF44.5 x ORF44 <NA>
## 1291333: EHV-1_8h_3 538465 ORF14 o ORF14 <NA>
## 1291334: EHV-1_8h_3 538469 ORF52 5`-short ORF52 CAGE_cluster_1624
## 1291335: EHV-1_8h_3 538479 ORF34 x ORF34 <NA>
## CAGE_significance support score CAGE.cluster.start
## <char> <int> <num> <int>
## 1: *** 7 1903.5173 135914
## 2: *** 9 21752.1102 21199
## 3: *** 9 21752.1102 21199
## 4: <NA> NA NA NA
## 5: <NA> NA NA NA
## ---
## 1291331: <NA> NA NA NA
## 1291332: <NA> NA NA NA
## 1291333: <NA> NA NA NA
## 1291334: ** 4 980.0626 94075
## 1291335: <NA> NA NA NA
## CAGE.cluster.end seqnames strand TR_start TR_end correct_tss
## <int> <char> <char> <int> <int> <lgcl>
## 1: 135939 NC_001491.2 + 135915 136464 FALSE
## 2: 21211 NC_001491.2 - 20380 21209 TRUE
## 3: 21211 NC_001491.2 - 20380 21209 FALSE
## 4: NA NC_001491.2 + 138461 138877 FALSE
## 5: NA NC_001491.2 + 138461 138877 TRUE
## ---
## 1291331: NA NC_001491.2 - 16999 18170 FALSE
## 1291332: NA NC_001491.2 + 82705 83094 FALSE
## 1291333: NA NC_001491.2 + 18235 19534 TRUE
## 1291334: 94076 NC_001491.2 - 93038 94076 FALSE
## 1291335: NA NC_001491.2 - 65085 65256 FALSE
## correct_tes count rep hpi Time cell_line group prime3.TR
## <lgcl> <int> <int> <fctr> <int> <fctr> <char> <int>
## 1: TRUE 4 1 12h 12 RK-13 RK-13_12h 136464
## 2: TRUE 324 1 12h 12 RK-13 RK-13_12h 20380
## 3: TRUE 56 1 12h 12 RK-13 RK-13_12h 20380
## 4: TRUE 4 1 12h 12 RK-13 RK-13_12h 138877
## 5: TRUE 1 1 12h 12 RK-13 RK-13_12h 138877
## ---
## 1291331: FALSE 1 3 8h 8 RK-13 RK-13_8h 16999
## 1291332: TRUE 1 3 8h 8 RK-13 RK-13_8h 83094
## 1291333: FALSE 1 3 8h 8 RK-13 RK-13_8h 19534
## 1291334: TRUE 1 3 8h 8 RK-13 RK-13_8h 93038
## 1291335: TRUE 1 3 8h 8 RK-13 RK-13_8h 65085
## prime5.TR
## <int>
## 1: 135915
## 2: 21209
## 3: 21209
## 4: 138461
## 5: 138461
## ---
## 1291331: 18170
## 1291332: 82705
## 1291333: 18235
## 1291334: 94076
## 1291335: 65256## [1] 538026## [1] 112945
## [1] 1254## [1] 1039## [1] 785## [1] 613## [1] 463## [1] 315## [1] 298## CAGE_significance support N
## <char> <int> <int>
## 1: ** 3 93
## 2: *** 3 68
## 3: ** 5 86
## 4: * 2 266
## 5: * 1 434
## 6: ** 4 84
## 7: *** 7 47
## 8: *** 9 80
## 9: *** 8 43
## 10: *** 6 53
Annotation plotting function
With annnotation
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Tests
